01.12.14 10:45 AM ET

“Syria, Iraq, Egypt and other areas of the Holy Land sometimes overflow with tears,” Pope Francis said at a meeting last November at the Vatican with leaders from Eastern rite churches that have links with the Roman Catholic Church. In May, the Pontiff will have a chance to witness those tears firsthand in Jordan, Israel and the West Bank when he becomes the fourth pope since Biblical times to visit the Holy Land.

Pope Francis’s trip to Amman, Jerusalem and Bethlehem was announced last week and will mark the 50th anniversary of a historic trip to the region by Pope Paul VI. It was during that visit that Paul met with the Ecumenical Patriarch Athenagoras to end officially the 900-year-long Great Schism between the churches of the East and West. But no one expects Pope Francis to pull off any historic reconciliation between Muslims and Christians—or even to be able to do much to bridge the vicious gap between Israelis and Palestinians. As the Pope has no divisions to field, all he will be able to do is to bear witness and to try to highlight the plight of Christianity in many of the Arab Spring states.

The announcement of Pope Francis’s Holy Land visit coincided with a depressing report from Open Doors, a non-denominational group supporting persecuted Christians worldwide. The group’s annual survey noted that the number of Christians killed for their faith doubled in 2013 from the year before, with Syria accounting for half of the documented 2,123 “martyr” killings.

The group acknowledged their count is “very minimal” and based on what they have been able to confirm. Other Christian groups put the annual figure in 2013 as high as 8,000 deaths with most coming in turbulent Middle East or African states where the majority religion is Islam.&nbsp; Michel Varton, head of Open Doors France, told journalists in Strasbourg that failing states with civil wars or violent internal tensions were the most dangerous for Christians, citing Syria as the worst example.

“In Syria, another war is thriving in the shadow of the civil war—the war against the church,” he said. “Islamist extremism is the worst persecutor of the worldwide church.” That persecution in the shadow of civil war has seen a mass Christian exodus with Christian refugees retreading the steps of their persecuted forebears and fleeing into southern Turkey for sanctuary. The civil war has seen half-a-million flee—nearly a quarter of Syria’s Christians—with more arriving in Turkey and Lebanon each day.

And fears are mounting that the sectarian conflict to oust President Bashar al-Assad could spell the doom of Syrian Christianity, in much the same way as Christianity has been severely damaged in Iraq, where after the fall of Saddam Hussein, sectarian killings, persecution of Christians and an increasingly Islamist political culture propelled more than half of the Iraqi Christian population to flee.

Before the civil war, Syria had an estimated Christian population of 2.5 million with the Greek Orthodox Church accounting for the largest share. The country also contained Catholics and Syriac Christians as well as Protestants and adherents of the Assyrian Church of the East.

Christian refugees in southern Turkey tell of rapes, forced conversions to Islam and the desecration of churches. Several clergy have been abducted, including two bishops. One of the worst atrocities was reported in the autumn with the Syriac Orthodox Archbishop of Homs, Selwanos Boutros Alnemeh, accusing jihadists of killing more than 40 Christians during their occupation of the town of Sadad, north of Damascus.

The Christians who make it out say they will never return. Forty-year-old Oarda Saliba, who fled from a village in Idlib province in northern Syria with her five daughters, ranging in age from 20 to five-years-old, says she will not go back. “We lived in fear. I was worried for the girls and wouldn’t let them go out. In a neighboring village, Christian girls were raped,” she says, sitting in a cold apartment the family rents with help from local Christians in the southern Turkish town of Midyat. She hopes Sweden or Germany will take them in. Even in Midyat, the family doesn’t feel entirely safe and the girls say that at the local school they are taunted and told they should convert to Islam.

Syria is seeing the worst of violence towards Christians in the region but across the Middle East and North Africa, alarm is rising. Last month, Prince Charles delivered an impassioned speech saying that that Christians in the Middle East are being “deliberately targeted by fundamentalist Islamist militants” and warning that Christianity is at risk of dying out in its birthplace.

In his November meeting with leaders from the Eastern rite churches, the Pope said, “We won’t resign ourselves to a Middle East without Christians who, for two thousand years, confess the name of Jesus as full citizens in social, cultural and religious life of the nations to which they belong.”

But as turmoil worsens in the region, the plight of Christians becomes more precarious. Open Doors in its annual survey could glimpse nothing to be optimistic about, pointing to “a strong drive to purge Christianity from Somalia” and Islamist attacks on Iraqi Christians in what had been a relatively safe area for them in the semi-autonomous Kurdish north of Iraq.

The killings the group documented are only the most extreme examples of anti-Christian persecution. Attacks on churches and associated schools, discrimination, threats and sexual assaults are growing more common across the Middle East.

In Egypt this past summer, after the military’s ouster of president Mohamed Morsi, Coptic churches and Christian institutions as well as property owned by Copts came under attack in what Bishop Anba Suriel, the bishop for the Coptic Orthodox Church in Melbourne in Australia, described as “unprecedented in the modern era.” Like many Christian leaders, he complains that the international media has failed to report enough on what is happening to the Middle East’s Christians and denounces of a lack of action by Western governments.

Top Islamist preachers and jihadists have added fuel to the raging anti-Christian fires. Sheikh Yusif al-Qaradawi, considered the spiritual father of the Muslim Brotherhood, urged retaliation against the Copts for their backing of the Egyptian military, posting an online video saying that Christians “were recruited [by Egypt’s military] to kill innocent Muslims.”

And Al-Qaeda leader Ayman al-Zawahiri accused Coptic Pope Tawadros II of wanting to establish a Coptic state in Egypt.

In neighboring Libya, the decision by the country’s assembly that its coming constitution must be based on Sharia law is adding to anxiety about the prospects for Christians in Libya, which is experiencing a rapid rise in Islamist sentiment. Three communities of Roman Catholic nuns left Libya last spring amid concerns for their safety because of threats from radical Islamists. One of the departing communities—the Congregation of the Holy Family of Spoleto – had worked for nearly a century in the town of Derna, east of Benghazi, a hotbed of Islamist sentiment.

“The religious sisters felt they had to leave—they felt they were in danger,” said Father Dominique, a priest in Tripoli and a former Vatican diplomat. Before the fall of Muammar Gaddafi, an estimated 100,000 Christians lived in Libya, mainly Copts and nearly all of them foreign workers, but religious leaders say more than half of them have now gone. There has been little violence but a lot of intimidation, although a year ago two Egyptian Copts were killed in a bomb blast at a Coptic church in the Mediterranean town of Dafniya.

Basem Shabb, a Lebanese lawmaker and the only Protestant in Lebanon’s Parliament, argues that much of the persecution of Christians in the region stems from their support of the past autocrat regimes. “It was a strategic error to tie their fates to those regimes.” But other Christian leaders maintain that, as vulnerable minorities, they had little choice but to do so.

The big question is how many Christian communities will be left in the Middle East when the next Pope visits the region.